Getting Started - Revision history

Frodo at 06:37, 13 March 2014

2014-03-13T06:37:40Z

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	[[Category:Docking]]		[[Category:Docking]]
	~~[[Category:Theory]]~~

Frodo at 03:44, 14 February 2014

2014-02-14T03:44:31Z

← Older revision		Revision as of 03:44, 14 February 2014
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	[[Only have a shaky homology model]]		[[Only have a shaky homology model]]


			[[Category:Docking]]
			[[Category:Theory]]

Therese: 4 revisions

2012-10-08T20:25:24Z

4 revisions

← Older revision

Revision as of 20:25, 8 October 2012

Frodo at 17:42, 21 September 2006

2006-09-21T17:42:42Z

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	Before docking, you should take a close look at the [[features of your target structure]].		Before docking, you should take a close look at the [[features of your target structure]].

	You should collect together any [[activity data] you may have.		You should collect together any [[activity data]] you may have.

	You should consider [[which database subset to dock]].		You should consider [[which database subset to dock]].

Frodo at 17:42, 21 September 2006

2006-09-21T17:42:23Z

@@ Line 4: / Line 4: @@
 Docking requires a structure of the target to dock to.
-== Target structure available ==
+== Target structure NOT available ==
 If you have only one structure available, then that is probably the one you should use. If you have more than one structure, then you will probably need to pick a single structure to dock to. You may also be able to use multiple structures in various ways to inform your docking.
 Generally, ligand-bound crystal structures are preferable to apo-enzyme crystal structures, which in turn are preferable to NMR structures, which in turn are preferable to homology or hand-built models. High resolution, problem free structures are better than lower resolution structures, or structures with problems.
-== Target structure unavailable ==
 Before docking, you should take a close look at the [[features of your target structure]].

Frodo: /* Target structure unavailable */

2006-09-21T17:24:12Z

Target structure unavailable

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	You may still be able to dock to a homology model of your target, if you know the sequence. Try using [http://salilab.org ModBase].		You may still be able to dock to a homology model of your target, if you know the sequence. Try using [http://salilab.org ModBase].

	Before docking, you should take a close look at the [[features of your ~~crystal~~ structure]].		Before docking, you should take a close look at the [[features of your target structure]].

Frodo at 03:43, 21 September 2006

2006-09-21T03:43:12Z

New page

=Getting Started with Docking=
There are exceptions to every rule. Please do not use this guide as a substitute for common sense.

Docking requires a structure of the target to dock to.

== Target structure available ==
If you have only one structure available, then that is probably the one you should use. If you have more than one structure, then you will probably need to pick a single structure to dock to. You may also be able to use multiple structures in various ways to inform your docking.

Generally, ligand-bound crystal structures are preferable to apo-enzyme crystal structures, which in turn are preferable to NMR structures, which in turn are preferable to homology or hand-built models. High resolution, problem free structures are better than lower resolution structures, or structures with problems.

== Target structure unavailable ==
You may still be able to dock to a homology model of your target, if you know the sequence. Try using [http://salilab.org ModBase].

Before docking, you should take a close look at the [[features of your crystal structure]].